Pekka
Having read the stream so far, it seems that you want to create an application that somehow authenticates with the server - i.e. the "average user" will not have access to it. If so, then delivering it through the browser is not possible without writing a user extension.
Starting authentication through GreaseMonkey is difficult, but once the client is authenticated, there is no real way to “start” the trace.
If the server creates a batch file or any set of commands (script, shortcut, etc.), you can simply configure the browser (or configure the browser for the local instance of your application) to run the file. The problem is that you don’t have the ability to automatically authenticate!
The only other way I can imagine that you can make it work is with the Java applet, which will be cumbersome and require that Java be initialized every time you want to import a trace.
The problem is that the browser is intrinsically secure. It is designed to protect your computer from malware, rogue sites, etc. Etc., Therefore, without developing a custom extension for the browser, there is no way to make a jump for any applications that work in tandem with the browser.
So, on this note, I suggest you reconsider writing the XUL Firefox extension, as mentioned above. You will probably need to implement some XPCOM code for it to work too. Here are some resources to help you get started:
https://developer.mozilla.org/en/xpcom
https://developer.mozilla.org/En/XUL
http://ted.mielczarek.org/code/mozilla/extensiondev/
https://developer.mozilla.org/en/XUL_Tutorial/Introduction